fastpathz cannot traverse the network: TypeError: no path to target

[jmeppley]

Running phanotate on some phage gives me this error. The below is from Hubei odonate virus 11:

(phan.env) [jmeppley@tyrosine phanotate]$ phanotate.py -o test/NC_032956.ncbi.faa -f fasta test/NC_032956.ncbi.fasta 
/mnt/data0/jmeppley/projects/nanopore_biller/viemes_by_depth/phage_clusters/phanotate/phan.env/bin/phanotate.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('phanotate==1.6.3')
Traceback (most recent call last):
  File "/mnt/data0/jmeppley/projects/nanopore_biller/viemes_by_depth/phage_clusters/phanotate/phan.env/bin/phanotate.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/mnt/data0/jmeppley/projects/nanopore_biller/viemes_by_depth/phage_clusters/phanotate/PHANOTATE/phanotate.py", line 63, in <module>
    shortest_path = fz.get_path(source=source, target=target)
TypeError: No path to target

I have seen the error in phanotate version 1.5.1 (python 3.7 and 3.10) and the latest from github (1.6.3) on python 3.10.

[deprekate]

hm, looking at the genome, I am pretty sure it is caused by this giant 500bp of noncoding space between gp2 and gp3

I have the tolerance for noncoding gaps currently hard set at 300bp. Usually there are spurious false positive ORFs that allow the FASTPATH to jump such gaps, but it appears there is not a single possible ORF within that region.

To verify my suspicion, I fudge the genome a little to introduce a tiny ORF between the gp2 and gp3 genes by changing the internal stop codon in the pink/yellow region to an AGA and it allowed phanotate to jump the gap:

$ phanotate.py fudged.fasta 
#id:	NC_032956
#START	STOP	FRAME	CONTIG	SCORE
156	6662	+	NC_032956	-3.116770851669423876397960614E+48	
6769	8730	+	NC_032956	-3856076414883.260858535901140	
8885	8986	+	NC_032956	-2.694481252924878820091418773	
9152	9030	-	NC_032956	-0.1392390679612810770032495566	
9238	10590	+	NC_032956	-4207404799.216605188066453756	
10857	10693	-	NC_032956	-53.14899699753530574312845421	
10928	11035	+	NC_032956	-1.287255596423134590081672391	
11017	11205	+	NC_032956	-25.86378478556807501777759741	
11257	11349	+	NC_032956	-5.693152356918419510588396127	

I have the gap limit set to 500bp in the phanotate 2.1 version (which also allows it to run successfully on the genome without fudging it), but I haven't gotten around to pushing that version to the main branch here or pypi due to other errors that I was not able to debug since the genomes that crashed it were not publicly available to me. In the meantime I should update the 1.X version to have a large gap.

[jmeppley]

That did the trick for me. Thanks.